[BioC] how to use limma on this format

Weiwei Shi helprhelp at gmail.com
Tue Jul 17 01:45:19 CEST 2007

Hi, there:

I have an agilent data format with colnames which look like the
followings. I am wondering how to proceed with this data by using
limma to do the QC. I mean, I probably can create some corresponding
objects of limma manually (like RGList from gMedianSignal...) but it
is painful. Anyone knows about this source or any suggestions to move
from there.

Another question, can I find "locuslink id" for ProbeName for agilent?


the data columns are
> as.character(t0[9,])
 [1] "FEATURES"                       "FeatureNum"
 [4] "Col"                            "Start"
 [7] "ProbeUID"                       "ControlType"
[10] "GeneName"                       "PositionX"
[13] "LogRatio"                       "LogRatioError"
[16] "gSurrogateUsed"                 "rSurrogateUsed"
[19] "rIsFound"                       "gProcessedSignal"
[22] "gProcessedSigError"             "rProcessedSigError"
[25] "rNumPixOLHi"                    "gNumPixOLLo"
[28] "gNumPix"                        "rNumPix"
[31] "rMeanSignal"                    "gMedianSignal"
[34] "gPixSDev"                       "rPixSDev"
[37] "rBGNumPix"                      "gBGMeanSignal"
[40] "gBGMedianSignal"                "rBGMedianSignal"
[43] "rBGPixSDev"                     "gNumSatPix"
[46] "gIsSaturated"                   "rIsSaturated"
[49] "BGPixCorrelation"               "gIsFeatNonUnifOL"
[52] "gIsBGNonUnifOL"                 "rIsBGNonUnifOL"
[55] "rIsFeatPopnOL"                  "gIsBGPopnOL"
[58] "IsManualFlag"                   "gBGSubSignal"
[61] "gBGSubSigError"                 "rBGSubSigError"
[64] "gIsPosAndSignif"                "rIsPosAndSignif"
[67] "rPValFeatEqBG"                  "gNumBGUsed"
[70] "gIsWellAboveBG"                 "rIsWellAboveBG"
[73] "rBGUsed"                        "gBGSDUsed"
[76] "IsNormalization"                "gDyeNormSignal"
[79] "gDyeNormError"                  "rDyeNormError"
[82] "ErrorModel"                     "xDev"
[85] "rSpatialDetrendIsInFilteredSet" "gSpatialDetrendSurfaceValue"
[88] ""                               ""

Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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